The request names scvi-tools, which is itself a Python library for probabilistic single-cell omics modelling; its listing is indexed as a skill under K-Dense 2 ("Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration" 12). Alternatives that do similar single-cell analysis are Scanpy-based tools listed under K-Dense 2 and GPTomics 4.
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scvi-tools (via K-Dense)k-dense.aiverified and signed
Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq and MultiVI RNA/ATAC integration 12.
for agents: scvi-tools · scanpy · scvelo
- 2
GPTomics single-cell agent skillsgptomics.comverified and signed
Provides single-cell trajectory inference and data IO skills covering Monocle3, Slingshot, scVelo and Scanpy for single-cell RNA-seq analysis 14.
for agents: bio-single-cell-trajectory-inference · bio-single-cell-data-io · bio-single-cell-cell-annotation
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Sources
- 2K-Dense | AI Agents for Real Researchk-dense.ai · read 2026-10-30
- 3singlet.bio — AI-ready single-cell data, at your fingertips.singlet.bio · read 2026-10-30
- 4GPTomics | AI neolab for Biologygptomics.com · read 2026-10-30
- 12scvi-tools: declares "scvi-tools" (the record we read and signed)unfragile.ai · read 2026-10-24
- 14bio-single-cell-trajectory-inference: declares "bio-single-cell-trajectory-inference" (the record we read and signed)unfragile.ai · read 2026-10-24
For agents: the 10 actions behind this answer
single-cell-rna-qc · single-cell-rna-qc verified and signed
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for si
scvi-tools · scvi-tools verified and signed
Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. Use for generative modeling, reference mapping, multimodal analysis, or model-based uncertainty; use scanpy for
singlet_search · singlet found in code, not yet checked
Search for single-cell RNA-seq samples in the Singlet Atlas.
bio-single-cell-trajectory-inference · bio-single-cell-trajectory-inference verified and signed
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis. Use when inferring developmental trajectories or pseudotime.
lobster-bioinformatics · lobster-bioinformatics verified and signed
Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization. Use when analyzing genomics data, searching for papers/datasets, or working with H5AD, CSV, GEO/SRA accessions, or biological data. Requires lob
· Async website read, tools not yet checked
A Rust library for easy and understandable async programming
· Omnilib website read, tools not yet checked
· lxml website read, tools not yet checked
lxml - the most feature-rich and easy-to-use library for processing XML and HTML in the Python language
· scikit-image website read, tools not yet checked
osdr_plot_top_rna · ai4ls found in code, not yet checked
Plot top 10 RNA counts and summarize for a dataset from the OSDR unnormalized counts API.
Labels are the instruments' verdict and are never changed by ranking. Agents and robots get this same answer as JSON at /api/v1/find?q=…&answer=1 and through the MCP server.